Multiple sequence alignment - TraesCS6B01G452300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G452300 chr6B 100.000 4201 0 0 1 4201 711334932 711330732 0.000000e+00 7758.0
1 TraesCS6B01G452300 chr6B 94.292 1962 73 19 891 2840 710684171 710682237 0.000000e+00 2966.0
2 TraesCS6B01G452300 chr6B 93.490 1106 38 8 2078 3177 710909233 710910310 0.000000e+00 1613.0
3 TraesCS6B01G452300 chr6B 81.667 1560 228 29 1479 3030 711756439 711757948 0.000000e+00 1243.0
4 TraesCS6B01G452300 chr6B 94.884 645 32 1 2629 3272 711382702 711383346 0.000000e+00 1007.0
5 TraesCS6B01G452300 chr6B 83.419 971 144 13 1481 2439 710642124 710641159 0.000000e+00 885.0
6 TraesCS6B01G452300 chr6B 95.150 433 13 1 479 903 710684621 710684189 0.000000e+00 676.0
7 TraesCS6B01G452300 chr6B 95.429 350 4 4 2977 3316 710664253 710663906 7.940000e-152 547.0
8 TraesCS6B01G452300 chr6B 96.818 220 6 1 491 710 711762457 711762675 2.390000e-97 366.0
9 TraesCS6B01G452300 chr6B 98.611 144 2 0 2838 2981 710666126 710665983 5.390000e-64 255.0
10 TraesCS6B01G452300 chr6B 85.232 237 35 0 1117 1353 711756200 711756436 1.170000e-60 244.0
11 TraesCS6B01G452300 chr6B 89.404 151 14 2 330 479 711762191 711762340 5.540000e-44 189.0
12 TraesCS6B01G452300 chr6B 94.118 119 6 1 1 119 711761991 711762108 3.340000e-41 180.0
13 TraesCS6B01G452300 chr6B 91.860 86 7 0 215 300 615364043 615364128 2.050000e-23 121.0
14 TraesCS6B01G452300 chr6B 78.286 175 29 7 537 711 711723558 711723723 2.070000e-18 104.0
15 TraesCS6B01G452300 chr6A 96.036 2750 60 14 574 3316 612171833 612169126 0.000000e+00 4429.0
16 TraesCS6B01G452300 chr6A 84.303 1822 197 45 709 2466 612290955 612292751 0.000000e+00 1698.0
17 TraesCS6B01G452300 chr6A 84.895 1708 202 29 759 2432 611901626 611903311 0.000000e+00 1674.0
18 TraesCS6B01G452300 chr6A 86.523 1254 155 3 964 2217 125260090 125261329 0.000000e+00 1367.0
19 TraesCS6B01G452300 chr6A 81.302 1567 222 49 1481 3031 612300512 612302023 0.000000e+00 1205.0
20 TraesCS6B01G452300 chr6A 83.218 435 70 3 2582 3015 125261615 125262047 3.040000e-106 396.0
21 TraesCS6B01G452300 chr6A 82.831 431 71 3 2586 3015 611903389 611903817 2.370000e-102 383.0
22 TraesCS6B01G452300 chr6D 95.238 2289 81 14 1049 3316 466227298 466225017 0.000000e+00 3598.0
23 TraesCS6B01G452300 chr6D 84.126 1808 187 57 713 2461 466328839 466330605 0.000000e+00 1657.0
24 TraesCS6B01G452300 chr6D 83.648 954 138 13 1481 2423 465744259 465743313 0.000000e+00 881.0
25 TraesCS6B01G452300 chr6D 82.000 300 51 2 2582 2878 466330684 466330983 6.970000e-63 252.0
26 TraesCS6B01G452300 chr6D 84.865 185 28 0 2692 2876 465743105 465742921 1.990000e-43 187.0
27 TraesCS6B01G452300 chr6D 82.530 166 15 6 149 300 192114493 192114658 2.640000e-27 134.0
28 TraesCS6B01G452300 chr6D 94.915 59 3 0 574 632 466227363 466227305 4.470000e-15 93.5
29 TraesCS6B01G452300 chr6D 97.500 40 1 0 491 530 466227416 466227377 7.540000e-08 69.4
30 TraesCS6B01G452300 chr7D 94.927 887 44 1 3316 4201 579201984 579202870 0.000000e+00 1387.0
31 TraesCS6B01G452300 chr2D 94.921 886 45 0 3316 4201 483641675 483640790 0.000000e+00 1387.0
32 TraesCS6B01G452300 chr3B 93.912 887 53 1 3316 4201 825546817 825547703 0.000000e+00 1338.0
33 TraesCS6B01G452300 chr3B 92.897 887 62 1 3316 4201 26054412 26053526 0.000000e+00 1288.0
34 TraesCS6B01G452300 chr3B 92.446 887 66 1 3316 4201 25918303 25917417 0.000000e+00 1266.0
35 TraesCS6B01G452300 chr3B 92.446 887 66 1 3316 4201 26243414 26242528 0.000000e+00 1266.0
36 TraesCS6B01G452300 chr1A 92.801 889 62 2 3314 4201 276266616 276265729 0.000000e+00 1286.0
37 TraesCS6B01G452300 chr1A 92.688 889 62 2 3316 4201 52471399 52470511 0.000000e+00 1279.0
38 TraesCS6B01G452300 chr1A 92.334 887 67 1 3316 4201 468416988 468416102 0.000000e+00 1260.0
39 TraesCS6B01G452300 chr1B 81.667 180 30 2 301 478 183390039 183390217 3.380000e-31 147.0
40 TraesCS6B01G452300 chr1B 81.667 180 30 2 301 478 183445331 183445509 3.380000e-31 147.0
41 TraesCS6B01G452300 chr1B 89.535 86 9 0 215 300 288157728 288157813 4.440000e-20 110.0
42 TraesCS6B01G452300 chr4A 81.215 181 30 4 301 479 727848556 727848734 4.380000e-30 143.0
43 TraesCS6B01G452300 chr4A 97.222 36 0 1 488 522 594050406 594050371 4.540000e-05 60.2
44 TraesCS6B01G452300 chr1D 80.874 183 33 2 301 482 46338146 46337965 4.380000e-30 143.0
45 TraesCS6B01G452300 chr1D 81.875 160 15 6 155 300 206049176 206049335 5.700000e-24 122.0
46 TraesCS6B01G452300 chr7A 83.333 162 13 2 153 300 110548560 110548721 2.040000e-28 137.0
47 TraesCS6B01G452300 chr7A 82.209 163 15 2 150 298 35007403 35007565 1.230000e-25 128.0
48 TraesCS6B01G452300 chr2B 92.941 85 5 1 215 299 80376284 80376201 5.700000e-24 122.0
49 TraesCS6B01G452300 chr2B 93.750 48 3 0 3265 3312 66667635 66667682 5.830000e-09 73.1
50 TraesCS6B01G452300 chr5B 91.667 84 7 0 218 301 360766410 360766327 2.650000e-22 117.0
51 TraesCS6B01G452300 chr3D 90.476 84 8 0 215 298 250915678 250915761 1.230000e-20 111.0
52 TraesCS6B01G452300 chr3D 87.143 70 4 4 3246 3311 443364899 443364967 1.620000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G452300 chr6B 711330732 711334932 4200 True 7758.000000 7758 100.000000 1 4201 1 chr6B.!!$R2 4200
1 TraesCS6B01G452300 chr6B 710682237 710684621 2384 True 1821.000000 2966 94.721000 479 2840 2 chr6B.!!$R4 2361
2 TraesCS6B01G452300 chr6B 710909233 710910310 1077 False 1613.000000 1613 93.490000 2078 3177 1 chr6B.!!$F2 1099
3 TraesCS6B01G452300 chr6B 711382702 711383346 644 False 1007.000000 1007 94.884000 2629 3272 1 chr6B.!!$F3 643
4 TraesCS6B01G452300 chr6B 710641159 710642124 965 True 885.000000 885 83.419000 1481 2439 1 chr6B.!!$R1 958
5 TraesCS6B01G452300 chr6B 711756200 711757948 1748 False 743.500000 1243 83.449500 1117 3030 2 chr6B.!!$F5 1913
6 TraesCS6B01G452300 chr6B 710663906 710666126 2220 True 401.000000 547 97.020000 2838 3316 2 chr6B.!!$R3 478
7 TraesCS6B01G452300 chr6B 711761991 711762675 684 False 245.000000 366 93.446667 1 710 3 chr6B.!!$F6 709
8 TraesCS6B01G452300 chr6A 612169126 612171833 2707 True 4429.000000 4429 96.036000 574 3316 1 chr6A.!!$R1 2742
9 TraesCS6B01G452300 chr6A 612290955 612292751 1796 False 1698.000000 1698 84.303000 709 2466 1 chr6A.!!$F1 1757
10 TraesCS6B01G452300 chr6A 612300512 612302023 1511 False 1205.000000 1205 81.302000 1481 3031 1 chr6A.!!$F2 1550
11 TraesCS6B01G452300 chr6A 611901626 611903817 2191 False 1028.500000 1674 83.863000 759 3015 2 chr6A.!!$F4 2256
12 TraesCS6B01G452300 chr6A 125260090 125262047 1957 False 881.500000 1367 84.870500 964 3015 2 chr6A.!!$F3 2051
13 TraesCS6B01G452300 chr6D 466225017 466227416 2399 True 1253.633333 3598 95.884333 491 3316 3 chr6D.!!$R2 2825
14 TraesCS6B01G452300 chr6D 466328839 466330983 2144 False 954.500000 1657 83.063000 713 2878 2 chr6D.!!$F2 2165
15 TraesCS6B01G452300 chr6D 465742921 465744259 1338 True 534.000000 881 84.256500 1481 2876 2 chr6D.!!$R1 1395
16 TraesCS6B01G452300 chr7D 579201984 579202870 886 False 1387.000000 1387 94.927000 3316 4201 1 chr7D.!!$F1 885
17 TraesCS6B01G452300 chr2D 483640790 483641675 885 True 1387.000000 1387 94.921000 3316 4201 1 chr2D.!!$R1 885
18 TraesCS6B01G452300 chr3B 825546817 825547703 886 False 1338.000000 1338 93.912000 3316 4201 1 chr3B.!!$F1 885
19 TraesCS6B01G452300 chr3B 26053526 26054412 886 True 1288.000000 1288 92.897000 3316 4201 1 chr3B.!!$R2 885
20 TraesCS6B01G452300 chr3B 25917417 25918303 886 True 1266.000000 1266 92.446000 3316 4201 1 chr3B.!!$R1 885
21 TraesCS6B01G452300 chr3B 26242528 26243414 886 True 1266.000000 1266 92.446000 3316 4201 1 chr3B.!!$R3 885
22 TraesCS6B01G452300 chr1A 276265729 276266616 887 True 1286.000000 1286 92.801000 3314 4201 1 chr1A.!!$R2 887
23 TraesCS6B01G452300 chr1A 52470511 52471399 888 True 1279.000000 1279 92.688000 3316 4201 1 chr1A.!!$R1 885
24 TraesCS6B01G452300 chr1A 468416102 468416988 886 True 1260.000000 1260 92.334000 3316 4201 1 chr1A.!!$R3 885

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
273 274 0.035915 GGGGCTTGAGACTCCAACTC 60.036 60.000 0.00 0.00 35.26 3.01 F
279 280 0.105194 TGAGACTCCAACTCCCACCA 60.105 55.000 0.00 0.00 33.95 4.17 F
474 475 1.190643 ACTCACTGCTCTAAGCTCCC 58.809 55.000 0.11 0.00 42.97 4.30 F
1263 1450 1.214062 GAGACGGTGGAGTCAGCTG 59.786 63.158 7.63 7.63 43.24 4.24 F
2747 3024 1.139163 CAAATTTCAAGCACCACCGC 58.861 50.000 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1465 2.584791 CAAGCACTGATTGTAAACCGC 58.415 47.619 0.00 0.00 0.00 5.68 R
1282 1469 3.153919 GGTCCCAAGCACTGATTGTAAA 58.846 45.455 6.29 0.00 0.00 2.01 R
2650 2927 2.304092 TCTCCTGATCCATTTGCATGC 58.696 47.619 11.82 11.82 0.00 4.06 R
2824 3101 2.845659 ACACATCCCCTAGATTCACCA 58.154 47.619 0.00 0.00 30.59 4.17 R
3593 5641 0.478072 TGACAAACATCCAGGTGGCT 59.522 50.000 0.00 0.00 34.44 4.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.903855 CATGCCGACCCATCTGGC 60.904 66.667 0.00 0.00 41.83 4.85
30 31 0.323178 ATCTGGCCAGGTTTGCTCTG 60.323 55.000 32.23 3.70 0.00 3.35
68 69 2.578163 TTTCTCTCCATCGCAGGCCG 62.578 60.000 0.00 0.00 38.61 6.13
90 91 1.555533 CCCTCACCTAGAGTTTCACCC 59.444 57.143 0.00 0.00 43.12 4.61
161 162 8.520351 AGGTTTTTACAATATCCTTAACAGCAC 58.480 33.333 0.00 0.00 0.00 4.40
173 174 1.671901 AACAGCACGTTTGGTTGGGG 61.672 55.000 0.00 0.00 32.35 4.96
180 181 1.964933 ACGTTTGGTTGGGGGTAATTG 59.035 47.619 0.00 0.00 0.00 2.32
189 190 2.210644 TGGGGGTAATTGGAGTTAGGG 58.789 52.381 0.00 0.00 0.00 3.53
193 194 4.666431 GGGGGTAATTGGAGTTAGGGAATA 59.334 45.833 0.00 0.00 0.00 1.75
194 195 5.315109 GGGGGTAATTGGAGTTAGGGAATAT 59.685 44.000 0.00 0.00 0.00 1.28
195 196 6.246163 GGGGTAATTGGAGTTAGGGAATATG 58.754 44.000 0.00 0.00 0.00 1.78
209 210 6.803587 AGGGAATATGAATTGAAGGGGTAT 57.196 37.500 0.00 0.00 0.00 2.73
213 214 6.151817 GGAATATGAATTGAAGGGGTATGAGC 59.848 42.308 0.00 0.00 0.00 4.26
214 215 4.803329 ATGAATTGAAGGGGTATGAGCT 57.197 40.909 0.00 0.00 0.00 4.09
217 218 4.706476 TGAATTGAAGGGGTATGAGCTTTG 59.294 41.667 0.00 0.00 0.00 2.77
218 219 2.806945 TGAAGGGGTATGAGCTTTGG 57.193 50.000 0.00 0.00 0.00 3.28
219 220 1.992557 TGAAGGGGTATGAGCTTTGGT 59.007 47.619 0.00 0.00 0.00 3.67
221 222 3.589735 TGAAGGGGTATGAGCTTTGGTTA 59.410 43.478 0.00 0.00 0.00 2.85
222 223 3.933861 AGGGGTATGAGCTTTGGTTAG 57.066 47.619 0.00 0.00 0.00 2.34
223 224 2.509964 AGGGGTATGAGCTTTGGTTAGG 59.490 50.000 0.00 0.00 0.00 2.69
224 225 2.422945 GGGGTATGAGCTTTGGTTAGGG 60.423 54.545 0.00 0.00 0.00 3.53
225 226 2.422945 GGGTATGAGCTTTGGTTAGGGG 60.423 54.545 0.00 0.00 0.00 4.79
226 227 2.508300 GGTATGAGCTTTGGTTAGGGGA 59.492 50.000 0.00 0.00 0.00 4.81
227 228 3.053917 GGTATGAGCTTTGGTTAGGGGAA 60.054 47.826 0.00 0.00 0.00 3.97
228 229 4.386424 GGTATGAGCTTTGGTTAGGGGAAT 60.386 45.833 0.00 0.00 0.00 3.01
229 230 3.825908 TGAGCTTTGGTTAGGGGAATT 57.174 42.857 0.00 0.00 0.00 2.17
230 231 3.430453 TGAGCTTTGGTTAGGGGAATTG 58.570 45.455 0.00 0.00 0.00 2.32
231 232 2.760650 GAGCTTTGGTTAGGGGAATTGG 59.239 50.000 0.00 0.00 0.00 3.16
232 233 1.831106 GCTTTGGTTAGGGGAATTGGG 59.169 52.381 0.00 0.00 0.00 4.12
233 234 2.558800 GCTTTGGTTAGGGGAATTGGGA 60.559 50.000 0.00 0.00 0.00 4.37
234 235 3.785364 CTTTGGTTAGGGGAATTGGGAA 58.215 45.455 0.00 0.00 0.00 3.97
235 236 4.361783 CTTTGGTTAGGGGAATTGGGAAT 58.638 43.478 0.00 0.00 0.00 3.01
236 237 4.427956 TTGGTTAGGGGAATTGGGAATT 57.572 40.909 0.00 0.00 0.00 2.17
237 238 3.989056 TGGTTAGGGGAATTGGGAATTC 58.011 45.455 0.00 0.00 45.12 2.17
250 251 8.712228 GAATTGGGAATTCATAAGGGAATAGT 57.288 34.615 7.93 0.00 45.18 2.12
251 252 8.712228 AATTGGGAATTCATAAGGGAATAGTC 57.288 34.615 7.93 0.00 36.51 2.59
252 253 6.840090 TGGGAATTCATAAGGGAATAGTCA 57.160 37.500 7.93 0.00 36.51 3.41
253 254 7.406620 TGGGAATTCATAAGGGAATAGTCAT 57.593 36.000 7.93 0.00 36.51 3.06
254 255 7.233632 TGGGAATTCATAAGGGAATAGTCATG 58.766 38.462 7.93 0.00 36.51 3.07
255 256 6.660949 GGGAATTCATAAGGGAATAGTCATGG 59.339 42.308 7.93 0.00 36.51 3.66
256 257 6.660949 GGAATTCATAAGGGAATAGTCATGGG 59.339 42.308 7.93 0.00 36.51 4.00
257 258 5.582950 TTCATAAGGGAATAGTCATGGGG 57.417 43.478 0.00 0.00 0.00 4.96
258 259 3.330701 TCATAAGGGAATAGTCATGGGGC 59.669 47.826 0.00 0.00 0.00 5.80
259 260 1.912862 AAGGGAATAGTCATGGGGCT 58.087 50.000 0.00 0.00 0.00 5.19
260 261 1.912862 AGGGAATAGTCATGGGGCTT 58.087 50.000 0.00 0.00 0.00 4.35
261 262 1.496429 AGGGAATAGTCATGGGGCTTG 59.504 52.381 0.00 0.00 0.00 4.01
262 263 1.494721 GGGAATAGTCATGGGGCTTGA 59.505 52.381 0.00 0.00 0.00 3.02
263 264 2.487986 GGGAATAGTCATGGGGCTTGAG 60.488 54.545 0.00 0.00 0.00 3.02
264 265 2.439507 GGAATAGTCATGGGGCTTGAGA 59.560 50.000 0.00 0.00 0.00 3.27
265 266 3.471680 GAATAGTCATGGGGCTTGAGAC 58.528 50.000 0.00 0.00 0.00 3.36
266 267 2.254152 TAGTCATGGGGCTTGAGACT 57.746 50.000 0.00 0.00 41.88 3.24
267 268 0.908198 AGTCATGGGGCTTGAGACTC 59.092 55.000 0.00 0.00 34.71 3.36
268 269 0.107459 GTCATGGGGCTTGAGACTCC 60.107 60.000 0.00 0.00 0.00 3.85
269 270 0.547471 TCATGGGGCTTGAGACTCCA 60.547 55.000 0.00 0.00 0.00 3.86
270 271 0.329261 CATGGGGCTTGAGACTCCAA 59.671 55.000 0.00 0.00 29.35 3.53
271 272 0.329596 ATGGGGCTTGAGACTCCAAC 59.670 55.000 0.00 0.00 29.35 3.77
272 273 0.768221 TGGGGCTTGAGACTCCAACT 60.768 55.000 0.00 0.00 0.00 3.16
273 274 0.035915 GGGGCTTGAGACTCCAACTC 60.036 60.000 0.00 0.00 35.26 3.01
274 275 0.035915 GGGCTTGAGACTCCAACTCC 60.036 60.000 0.00 0.00 33.95 3.85
275 276 0.035915 GGCTTGAGACTCCAACTCCC 60.036 60.000 0.00 0.00 33.95 4.30
276 277 0.687354 GCTTGAGACTCCAACTCCCA 59.313 55.000 0.00 0.00 33.95 4.37
277 278 1.609320 GCTTGAGACTCCAACTCCCAC 60.609 57.143 0.00 0.00 33.95 4.61
278 279 1.002544 CTTGAGACTCCAACTCCCACC 59.997 57.143 0.00 0.00 33.95 4.61
279 280 0.105194 TGAGACTCCAACTCCCACCA 60.105 55.000 0.00 0.00 33.95 4.17
280 281 1.280457 GAGACTCCAACTCCCACCAT 58.720 55.000 0.00 0.00 0.00 3.55
281 282 1.630878 GAGACTCCAACTCCCACCATT 59.369 52.381 0.00 0.00 0.00 3.16
282 283 2.040412 GAGACTCCAACTCCCACCATTT 59.960 50.000 0.00 0.00 0.00 2.32
283 284 2.447047 AGACTCCAACTCCCACCATTTT 59.553 45.455 0.00 0.00 0.00 1.82
284 285 3.655777 AGACTCCAACTCCCACCATTTTA 59.344 43.478 0.00 0.00 0.00 1.52
285 286 4.292306 AGACTCCAACTCCCACCATTTTAT 59.708 41.667 0.00 0.00 0.00 1.40
286 287 5.010708 ACTCCAACTCCCACCATTTTATT 57.989 39.130 0.00 0.00 0.00 1.40
287 288 6.011981 AGACTCCAACTCCCACCATTTTATTA 60.012 38.462 0.00 0.00 0.00 0.98
288 289 6.557568 ACTCCAACTCCCACCATTTTATTAA 58.442 36.000 0.00 0.00 0.00 1.40
289 290 7.189087 ACTCCAACTCCCACCATTTTATTAAT 58.811 34.615 0.00 0.00 0.00 1.40
290 291 8.340757 ACTCCAACTCCCACCATTTTATTAATA 58.659 33.333 0.00 0.00 0.00 0.98
291 292 9.196139 CTCCAACTCCCACCATTTTATTAATAA 57.804 33.333 3.71 3.71 0.00 1.40
292 293 9.196139 TCCAACTCCCACCATTTTATTAATAAG 57.804 33.333 7.91 0.22 0.00 1.73
293 294 8.421002 CCAACTCCCACCATTTTATTAATAAGG 58.579 37.037 7.91 8.74 0.00 2.69
294 295 8.421002 CAACTCCCACCATTTTATTAATAAGGG 58.579 37.037 16.58 16.58 0.00 3.95
295 296 7.889178 ACTCCCACCATTTTATTAATAAGGGA 58.111 34.615 21.00 21.00 39.16 4.20
297 298 7.302184 TCCCACCATTTTATTAATAAGGGAGG 58.698 38.462 19.49 19.88 36.71 4.30
298 299 6.496911 CCCACCATTTTATTAATAAGGGAGGG 59.503 42.308 25.71 25.71 36.00 4.30
299 300 6.496911 CCACCATTTTATTAATAAGGGAGGGG 59.503 42.308 20.57 15.75 0.00 4.79
300 301 7.302184 CACCATTTTATTAATAAGGGAGGGGA 58.698 38.462 20.57 0.59 0.00 4.81
301 302 7.787424 CACCATTTTATTAATAAGGGAGGGGAA 59.213 37.037 20.57 7.86 0.00 3.97
302 303 7.787904 ACCATTTTATTAATAAGGGAGGGGAAC 59.212 37.037 20.57 0.00 0.00 3.62
303 304 8.010697 CCATTTTATTAATAAGGGAGGGGAACT 58.989 37.037 7.91 0.00 0.00 3.01
304 305 9.434275 CATTTTATTAATAAGGGAGGGGAACTT 57.566 33.333 7.91 0.00 0.00 2.66
313 314 9.475013 AATAAGGGAGGGGAACTTATATTAACT 57.525 33.333 0.00 0.00 36.64 2.24
314 315 7.782695 AAGGGAGGGGAACTTATATTAACTT 57.217 36.000 0.00 0.00 0.00 2.66
315 316 7.782695 AGGGAGGGGAACTTATATTAACTTT 57.217 36.000 0.00 0.00 0.00 2.66
316 317 7.813331 AGGGAGGGGAACTTATATTAACTTTC 58.187 38.462 0.00 0.00 0.00 2.62
317 318 7.002879 GGGAGGGGAACTTATATTAACTTTCC 58.997 42.308 0.00 0.00 33.15 3.13
318 319 7.147177 GGGAGGGGAACTTATATTAACTTTCCT 60.147 40.741 0.00 0.00 34.19 3.36
319 320 8.280084 GGAGGGGAACTTATATTAACTTTCCTT 58.720 37.037 0.00 0.00 34.19 3.36
320 321 9.121658 GAGGGGAACTTATATTAACTTTCCTTG 57.878 37.037 0.00 0.00 34.19 3.61
321 322 8.621073 AGGGGAACTTATATTAACTTTCCTTGT 58.379 33.333 0.00 0.00 34.19 3.16
322 323 8.900781 GGGGAACTTATATTAACTTTCCTTGTC 58.099 37.037 0.00 0.00 34.19 3.18
323 324 9.682465 GGGAACTTATATTAACTTTCCTTGTCT 57.318 33.333 0.00 0.00 34.19 3.41
328 329 8.882415 TTATATTAACTTTCCTTGTCTAGGCG 57.118 34.615 0.00 0.00 44.37 5.52
336 337 1.352156 CTTGTCTAGGCGCCGTCAAC 61.352 60.000 23.20 18.04 0.00 3.18
338 339 1.516603 GTCTAGGCGCCGTCAACTC 60.517 63.158 23.20 5.52 0.00 3.01
339 340 2.202756 CTAGGCGCCGTCAACTCC 60.203 66.667 23.20 0.00 0.00 3.85
345 346 2.029964 GCCGTCAACTCCCACGAA 59.970 61.111 0.00 0.00 38.32 3.85
355 356 1.210967 ACTCCCACGAACCAAACAAGA 59.789 47.619 0.00 0.00 0.00 3.02
363 364 7.027161 CCCACGAACCAAACAAGAAAATATAG 58.973 38.462 0.00 0.00 0.00 1.31
412 413 7.898014 ATTCCTATCATACGCCATACATAGA 57.102 36.000 0.00 0.00 0.00 1.98
459 460 9.379770 TCCCATATCTAATCTCAATACAACTCA 57.620 33.333 0.00 0.00 0.00 3.41
469 470 6.625362 TCTCAATACAACTCACTGCTCTAAG 58.375 40.000 0.00 0.00 0.00 2.18
470 471 5.171476 TCAATACAACTCACTGCTCTAAGC 58.829 41.667 0.00 0.00 42.82 3.09
471 472 5.047021 TCAATACAACTCACTGCTCTAAGCT 60.047 40.000 0.11 0.00 42.97 3.74
472 473 3.311486 ACAACTCACTGCTCTAAGCTC 57.689 47.619 0.11 0.00 42.97 4.09
474 475 1.190643 ACTCACTGCTCTAAGCTCCC 58.809 55.000 0.11 0.00 42.97 4.30
477 565 2.170187 CTCACTGCTCTAAGCTCCCATT 59.830 50.000 0.11 0.00 42.97 3.16
742 857 3.077519 AATCTTCGGAGGGGACGCG 62.078 63.158 3.53 3.53 0.00 6.01
1075 1258 7.333528 TCAAACTTGCACTTTTGAGACTTAT 57.666 32.000 15.00 0.00 36.92 1.73
1263 1450 1.214062 GAGACGGTGGAGTCAGCTG 59.786 63.158 7.63 7.63 43.24 4.24
1278 1465 2.895865 CTGCCTGCCATGCTCTCG 60.896 66.667 0.00 0.00 0.00 4.04
1282 1469 4.827087 CTGCCATGCTCTCGCGGT 62.827 66.667 6.13 0.00 39.65 5.68
1574 1813 4.218635 TCTCTTGAGCATGACGTTCTACTT 59.781 41.667 0.00 0.00 0.00 2.24
1578 1817 5.576447 TGAGCATGACGTTCTACTTGATA 57.424 39.130 0.00 0.00 0.00 2.15
1579 1818 5.582550 TGAGCATGACGTTCTACTTGATAG 58.417 41.667 0.00 0.00 0.00 2.08
1580 1819 5.357032 TGAGCATGACGTTCTACTTGATAGA 59.643 40.000 0.00 0.00 38.20 1.98
1581 1820 5.583495 AGCATGACGTTCTACTTGATAGAC 58.417 41.667 0.00 0.00 39.78 2.59
2650 2927 4.443978 AGGTAATGGATCATCCTTGTGG 57.556 45.455 4.96 0.00 37.46 4.17
2747 3024 1.139163 CAAATTTCAAGCACCACCGC 58.861 50.000 0.00 0.00 0.00 5.68
2824 3101 2.251642 GGCGTGTCTTGAAAGCGGT 61.252 57.895 0.00 0.00 0.00 5.68
2849 3126 5.145564 GTGAATCTAGGGGATGTGTACCTA 58.854 45.833 0.00 0.00 35.84 3.08
3451 5499 4.251760 CTTCGCGAGCTTGTGAGT 57.748 55.556 16.55 0.00 0.00 3.41
3559 5607 0.179111 TACGCTGCCGGATTCTTCTG 60.179 55.000 5.05 0.00 39.22 3.02
3593 5641 1.375396 CACCACCTTCGCATCGGAA 60.375 57.895 0.00 0.00 0.00 4.30
3775 5825 0.719015 TGTCCTCTTCCTCTCCCCAT 59.281 55.000 0.00 0.00 0.00 4.00
3941 5991 3.806521 CAGAAGACGGGCTTTGATAGATG 59.193 47.826 0.00 0.00 36.83 2.90
3963 6013 3.567164 GTGCTCATATATTGCCTTGCAGT 59.433 43.478 5.36 0.00 40.61 4.40
4037 6087 0.399454 ATAGCGCCTCTTGCATGGAT 59.601 50.000 2.29 0.00 41.33 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.077265 CAAACCTGGCCAGATGGGT 59.923 57.895 34.91 21.59 39.65 4.51
17 18 1.676967 GGGCTCAGAGCAAACCTGG 60.677 63.158 24.09 0.00 44.75 4.45
30 31 2.592861 GATGGCACGGATGGGCTC 60.593 66.667 0.00 0.00 0.00 4.70
68 69 1.066071 GTGAAACTCTAGGTGAGGGGC 60.066 57.143 0.00 0.00 46.72 5.80
130 131 9.690913 GTTAAGGATATTGTAAAAACCTAGGGT 57.309 33.333 14.81 2.44 37.65 4.34
131 132 9.689501 TGTTAAGGATATTGTAAAAACCTAGGG 57.310 33.333 14.81 0.00 0.00 3.53
138 139 8.101654 ACGTGCTGTTAAGGATATTGTAAAAA 57.898 30.769 0.00 0.00 0.00 1.94
142 143 6.092944 CCAAACGTGCTGTTAAGGATATTGTA 59.907 38.462 0.00 0.00 40.84 2.41
145 146 5.007682 ACCAAACGTGCTGTTAAGGATATT 58.992 37.500 15.54 0.00 40.84 1.28
158 159 1.108132 TTACCCCCAACCAAACGTGC 61.108 55.000 0.00 0.00 0.00 5.34
161 162 1.273886 CCAATTACCCCCAACCAAACG 59.726 52.381 0.00 0.00 0.00 3.60
173 174 9.588096 AATTCATATTCCCTAACTCCAATTACC 57.412 33.333 0.00 0.00 0.00 2.85
180 181 6.717084 CCCTTCAATTCATATTCCCTAACTCC 59.283 42.308 0.00 0.00 0.00 3.85
189 190 6.944862 AGCTCATACCCCTTCAATTCATATTC 59.055 38.462 0.00 0.00 0.00 1.75
193 194 4.803329 AGCTCATACCCCTTCAATTCAT 57.197 40.909 0.00 0.00 0.00 2.57
194 195 4.591321 AAGCTCATACCCCTTCAATTCA 57.409 40.909 0.00 0.00 0.00 2.57
195 196 4.098501 CCAAAGCTCATACCCCTTCAATTC 59.901 45.833 0.00 0.00 0.00 2.17
209 210 3.430453 CAATTCCCCTAACCAAAGCTCA 58.570 45.455 0.00 0.00 0.00 4.26
213 214 3.466395 TCCCAATTCCCCTAACCAAAG 57.534 47.619 0.00 0.00 0.00 2.77
214 215 3.925261 TTCCCAATTCCCCTAACCAAA 57.075 42.857 0.00 0.00 0.00 3.28
217 218 3.989056 TGAATTCCCAATTCCCCTAACC 58.011 45.455 2.27 0.00 45.23 2.85
218 219 6.267699 CCTTATGAATTCCCAATTCCCCTAAC 59.732 42.308 2.27 0.00 45.23 2.34
219 220 6.381250 CCTTATGAATTCCCAATTCCCCTAA 58.619 40.000 2.27 2.74 45.23 2.69
221 222 4.389034 CCCTTATGAATTCCCAATTCCCCT 60.389 45.833 2.27 0.00 45.23 4.79
222 223 3.903714 CCCTTATGAATTCCCAATTCCCC 59.096 47.826 2.27 0.00 45.23 4.81
223 224 4.814967 TCCCTTATGAATTCCCAATTCCC 58.185 43.478 2.27 0.00 45.23 3.97
224 225 7.730332 ACTATTCCCTTATGAATTCCCAATTCC 59.270 37.037 2.27 0.00 45.23 3.01
225 226 8.712228 ACTATTCCCTTATGAATTCCCAATTC 57.288 34.615 2.27 2.55 45.86 2.17
226 227 8.288812 TGACTATTCCCTTATGAATTCCCAATT 58.711 33.333 2.27 0.00 36.41 2.32
227 228 7.825709 TGACTATTCCCTTATGAATTCCCAAT 58.174 34.615 2.27 0.00 36.41 3.16
228 229 7.219601 TGACTATTCCCTTATGAATTCCCAA 57.780 36.000 2.27 0.00 36.41 4.12
229 230 6.840090 TGACTATTCCCTTATGAATTCCCA 57.160 37.500 2.27 0.00 36.41 4.37
230 231 6.660949 CCATGACTATTCCCTTATGAATTCCC 59.339 42.308 2.27 0.00 36.41 3.97
231 232 6.660949 CCCATGACTATTCCCTTATGAATTCC 59.339 42.308 2.27 0.00 36.41 3.01
232 233 6.660949 CCCCATGACTATTCCCTTATGAATTC 59.339 42.308 0.00 0.00 36.41 2.17
233 234 6.555711 CCCCATGACTATTCCCTTATGAATT 58.444 40.000 0.00 0.00 36.41 2.17
234 235 5.517299 GCCCCATGACTATTCCCTTATGAAT 60.517 44.000 0.00 0.00 38.47 2.57
235 236 4.202567 GCCCCATGACTATTCCCTTATGAA 60.203 45.833 0.00 0.00 0.00 2.57
236 237 3.330701 GCCCCATGACTATTCCCTTATGA 59.669 47.826 0.00 0.00 0.00 2.15
237 238 3.331889 AGCCCCATGACTATTCCCTTATG 59.668 47.826 0.00 0.00 0.00 1.90
238 239 3.613559 AGCCCCATGACTATTCCCTTAT 58.386 45.455 0.00 0.00 0.00 1.73
239 240 3.074857 AGCCCCATGACTATTCCCTTA 57.925 47.619 0.00 0.00 0.00 2.69
240 241 1.912862 AGCCCCATGACTATTCCCTT 58.087 50.000 0.00 0.00 0.00 3.95
241 242 1.496429 CAAGCCCCATGACTATTCCCT 59.504 52.381 0.00 0.00 0.00 4.20
242 243 1.494721 TCAAGCCCCATGACTATTCCC 59.505 52.381 0.00 0.00 0.00 3.97
243 244 2.439507 TCTCAAGCCCCATGACTATTCC 59.560 50.000 0.00 0.00 0.00 3.01
244 245 3.135530 AGTCTCAAGCCCCATGACTATTC 59.864 47.826 0.00 0.00 36.39 1.75
245 246 3.118531 AGTCTCAAGCCCCATGACTATT 58.881 45.455 0.00 0.00 36.39 1.73
246 247 2.703007 GAGTCTCAAGCCCCATGACTAT 59.297 50.000 0.00 0.00 38.00 2.12
247 248 2.111384 GAGTCTCAAGCCCCATGACTA 58.889 52.381 0.00 0.00 38.00 2.59
248 249 0.908198 GAGTCTCAAGCCCCATGACT 59.092 55.000 0.00 0.00 40.21 3.41
249 250 0.107459 GGAGTCTCAAGCCCCATGAC 60.107 60.000 1.47 0.00 0.00 3.06
250 251 0.547471 TGGAGTCTCAAGCCCCATGA 60.547 55.000 1.47 0.00 0.00 3.07
251 252 0.329261 TTGGAGTCTCAAGCCCCATG 59.671 55.000 1.47 0.00 0.00 3.66
252 253 0.329596 GTTGGAGTCTCAAGCCCCAT 59.670 55.000 1.47 0.00 0.00 4.00
253 254 0.768221 AGTTGGAGTCTCAAGCCCCA 60.768 55.000 1.47 0.00 0.00 4.96
254 255 0.035915 GAGTTGGAGTCTCAAGCCCC 60.036 60.000 1.47 0.00 32.79 5.80
255 256 0.035915 GGAGTTGGAGTCTCAAGCCC 60.036 60.000 1.47 0.00 34.04 5.19
256 257 0.035915 GGGAGTTGGAGTCTCAAGCC 60.036 60.000 1.47 0.00 34.04 4.35
257 258 0.687354 TGGGAGTTGGAGTCTCAAGC 59.313 55.000 1.47 0.00 34.04 4.01
258 259 1.002544 GGTGGGAGTTGGAGTCTCAAG 59.997 57.143 1.47 0.00 28.17 3.02
259 260 1.056660 GGTGGGAGTTGGAGTCTCAA 58.943 55.000 1.47 0.00 28.17 3.02
260 261 0.105194 TGGTGGGAGTTGGAGTCTCA 60.105 55.000 1.47 0.00 34.04 3.27
261 262 1.280457 ATGGTGGGAGTTGGAGTCTC 58.720 55.000 0.00 0.00 0.00 3.36
262 263 1.747444 AATGGTGGGAGTTGGAGTCT 58.253 50.000 0.00 0.00 0.00 3.24
263 264 2.586648 AAATGGTGGGAGTTGGAGTC 57.413 50.000 0.00 0.00 0.00 3.36
264 265 4.675063 ATAAAATGGTGGGAGTTGGAGT 57.325 40.909 0.00 0.00 0.00 3.85
265 266 7.660030 ATTAATAAAATGGTGGGAGTTGGAG 57.340 36.000 0.00 0.00 0.00 3.86
266 267 9.196139 CTTATTAATAAAATGGTGGGAGTTGGA 57.804 33.333 9.15 0.00 0.00 3.53
267 268 8.421002 CCTTATTAATAAAATGGTGGGAGTTGG 58.579 37.037 9.15 0.00 0.00 3.77
268 269 8.421002 CCCTTATTAATAAAATGGTGGGAGTTG 58.579 37.037 17.33 0.29 33.14 3.16
269 270 8.348354 TCCCTTATTAATAAAATGGTGGGAGTT 58.652 33.333 19.49 0.00 35.38 3.01
270 271 7.889178 TCCCTTATTAATAAAATGGTGGGAGT 58.111 34.615 19.49 0.00 35.38 3.85
272 273 7.302184 CCTCCCTTATTAATAAAATGGTGGGA 58.698 38.462 21.00 21.00 37.65 4.37
273 274 6.496911 CCCTCCCTTATTAATAAAATGGTGGG 59.503 42.308 25.43 25.43 35.42 4.61
274 275 6.496911 CCCCTCCCTTATTAATAAAATGGTGG 59.503 42.308 20.01 20.01 0.00 4.61
275 276 7.302184 TCCCCTCCCTTATTAATAAAATGGTG 58.698 38.462 9.15 9.92 0.00 4.17
276 277 7.488889 TCCCCTCCCTTATTAATAAAATGGT 57.511 36.000 9.15 0.00 0.00 3.55
277 278 8.010697 AGTTCCCCTCCCTTATTAATAAAATGG 58.989 37.037 9.15 9.65 0.00 3.16
278 279 9.434275 AAGTTCCCCTCCCTTATTAATAAAATG 57.566 33.333 9.15 1.70 0.00 2.32
287 288 9.475013 AGTTAATATAAGTTCCCCTCCCTTATT 57.525 33.333 0.00 0.00 34.26 1.40
288 289 9.475013 AAGTTAATATAAGTTCCCCTCCCTTAT 57.525 33.333 0.00 0.00 35.93 1.73
289 290 8.881109 AAGTTAATATAAGTTCCCCTCCCTTA 57.119 34.615 0.00 0.00 0.00 2.69
290 291 7.782695 AAGTTAATATAAGTTCCCCTCCCTT 57.217 36.000 0.00 0.00 0.00 3.95
291 292 7.147177 GGAAAGTTAATATAAGTTCCCCTCCCT 60.147 40.741 0.00 0.00 0.00 4.20
292 293 7.002879 GGAAAGTTAATATAAGTTCCCCTCCC 58.997 42.308 0.00 0.00 0.00 4.30
293 294 7.813331 AGGAAAGTTAATATAAGTTCCCCTCC 58.187 38.462 0.00 4.53 0.00 4.30
294 295 9.121658 CAAGGAAAGTTAATATAAGTTCCCCTC 57.878 37.037 0.00 0.00 0.00 4.30
295 296 8.621073 ACAAGGAAAGTTAATATAAGTTCCCCT 58.379 33.333 0.00 7.06 0.00 4.79
296 297 8.818622 ACAAGGAAAGTTAATATAAGTTCCCC 57.181 34.615 0.00 5.54 0.00 4.81
297 298 9.682465 AGACAAGGAAAGTTAATATAAGTTCCC 57.318 33.333 0.00 0.00 0.00 3.97
317 318 1.080093 TTGACGGCGCCTAGACAAG 60.080 57.895 26.68 9.51 0.00 3.16
318 319 1.373748 GTTGACGGCGCCTAGACAA 60.374 57.895 26.68 18.89 0.00 3.18
319 320 2.209064 GAGTTGACGGCGCCTAGACA 62.209 60.000 26.68 13.68 0.00 3.41
320 321 1.516603 GAGTTGACGGCGCCTAGAC 60.517 63.158 26.68 16.98 0.00 2.59
321 322 2.707849 GGAGTTGACGGCGCCTAGA 61.708 63.158 26.68 4.18 0.00 2.43
322 323 2.202756 GGAGTTGACGGCGCCTAG 60.203 66.667 26.68 12.89 0.00 3.02
323 324 3.766691 GGGAGTTGACGGCGCCTA 61.767 66.667 26.68 7.95 0.00 3.93
328 329 2.029964 TTCGTGGGAGTTGACGGC 59.970 61.111 0.00 0.00 36.23 5.68
336 337 1.961793 TCTTGTTTGGTTCGTGGGAG 58.038 50.000 0.00 0.00 0.00 4.30
338 339 3.512033 TTTTCTTGTTTGGTTCGTGGG 57.488 42.857 0.00 0.00 0.00 4.61
339 340 7.590279 ACTATATTTTCTTGTTTGGTTCGTGG 58.410 34.615 0.00 0.00 0.00 4.94
363 364 5.679734 TGTGAGAGCATTTGAGAAGAAAC 57.320 39.130 0.00 0.00 0.00 2.78
459 460 1.137872 CGAATGGGAGCTTAGAGCAGT 59.862 52.381 2.47 0.00 45.56 4.40
462 463 0.882484 GGCGAATGGGAGCTTAGAGC 60.882 60.000 0.00 0.00 42.84 4.09
661 768 4.235360 GAGACGGAATTCGAAAGAGTTGA 58.765 43.478 0.00 0.00 40.36 3.18
736 851 1.352156 CCTAGAGTTGTTGCGCGTCC 61.352 60.000 8.43 0.00 0.00 4.79
742 857 3.077359 ACTGATTGCCTAGAGTTGTTGC 58.923 45.455 0.00 0.00 0.00 4.17
788 905 4.514577 AAGTCCTCGCCATCGCCG 62.515 66.667 0.00 0.00 35.26 6.46
1096 1279 5.907866 TCAGAGTTGATATCACGGTACAA 57.092 39.130 4.48 0.00 0.00 2.41
1278 1465 2.584791 CAAGCACTGATTGTAAACCGC 58.415 47.619 0.00 0.00 0.00 5.68
1282 1469 3.153919 GGTCCCAAGCACTGATTGTAAA 58.846 45.455 6.29 0.00 0.00 2.01
2650 2927 2.304092 TCTCCTGATCCATTTGCATGC 58.696 47.619 11.82 11.82 0.00 4.06
2747 3024 6.176183 ACAGAAGATGATTAGTTTGGTCAGG 58.824 40.000 0.00 0.00 0.00 3.86
2824 3101 2.845659 ACACATCCCCTAGATTCACCA 58.154 47.619 0.00 0.00 30.59 4.17
2849 3126 5.479124 TGCTGCATGTCAGTCTATCATAT 57.521 39.130 15.48 0.00 44.66 1.78
3259 5305 3.745803 GGCTGCTGCTGCCTTGAC 61.746 66.667 34.54 14.47 43.62 3.18
3543 5591 0.449388 CAACAGAAGAATCCGGCAGC 59.551 55.000 0.00 0.00 0.00 5.25
3559 5607 4.080526 AGGTGGTGGTACAAGATATCCAAC 60.081 45.833 0.00 0.00 44.16 3.77
3593 5641 0.478072 TGACAAACATCCAGGTGGCT 59.522 50.000 0.00 0.00 34.44 4.75
3775 5825 5.050227 GCAAAGTTTAATGTTGATGCTGCAA 60.050 36.000 6.36 0.00 0.00 4.08
3941 5991 3.567164 ACTGCAAGGCAATATATGAGCAC 59.433 43.478 11.27 3.11 38.41 4.40
4037 6087 2.093128 GGATCCGAAGAGGTGGCTTTTA 60.093 50.000 0.00 0.00 41.99 1.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.